Last updated: 2025-09-07

Checks: 6 1

Knit directory: casper_ss_ma/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(12345)

The command set.seed(12345) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Cache: none

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File paths: absolute

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absolute relative
/hpcnfs/scratch/SS/zhan/casper_ss_ma/docs/figure ../docs/figure

Repository version: 8cc7ce7

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 8cc7ce7. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Unstaged changes:
    Modified:   casper_ss_ma.Rproj

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/resources.Rmd) and HTML (docs/resources.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html 8cc7ce7 Yinxiu Zhan 2025-09-07 Build site.
html c162f98 Yinxiu Zhan 2025-09-07 Build site.
html 86929e5 Yinxiu Zhan 2025-09-04 Build site.
Rmd 4ec8ace Yinxiu Zhan 2025-09-04 Add pvalue to aneuploidy vs CD82
html b9f5518 annamariapiva 2025-07-17 Build site.
html 7c37a58 annamariapiva 2025-07-17 Build site.
Rmd 33980ba annamariapiva 2025-07-17 updated resources
html 37a148c annamariapiva 2025-07-17 Build site.
Rmd 3016fe1 annamariapiva 2025-07-17 updated resources with link to raw data
html 08e59c3 annamariapiva 2025-06-25 Build site.
Rmd d6bf4f3 annamariapiva 2025-06-25 updated resources
html d711ff8 Yinxiu Zhan 2025-03-28 Build site.
html e5932bb Yinxiu Zhan 2025-03-28 Build site.
html 398ff3e Yinxiu Zhan 2025-03-28 Build site.
Rmd 1b4e94a Yinxiu Zhan 2025-03-28 add expression correlation

Figures

Download figures (ZIP archive) 

R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] vctrs_0.6.3       cli_3.6.1         knitr_1.44        rlang_1.1.1      
 [5] xfun_0.40         highr_0.10        stringi_1.7.12    promises_1.2.1   
 [9] jsonlite_1.8.7    workflowr_1.7.1   glue_1.6.2        rprojroot_2.0.3  
[13] git2r_0.32.0      htmltools_0.5.6   httpuv_1.6.11     sass_0.4.7       
[17] fansi_1.0.4       rmarkdown_2.24    jquerylib_0.1.4   evaluate_0.21    
[21] tibble_3.2.1      fastmap_1.1.1     yaml_2.3.7        lifecycle_1.0.3  
[25] whisker_0.4.1     stringr_1.5.0     compiler_4.3.1    fs_1.6.3         
[29] Rcpp_1.0.11       pkgconfig_2.0.3   rstudioapi_0.15.0 later_1.3.1      
[33] digest_0.6.33     R6_2.5.1          utf8_1.2.3        pillar_1.9.0     
[37] magrittr_2.0.3    bslib_0.5.1       tools_4.3.1       mime_0.12        
[41] cachem_1.0.8